Introducing the TE Hub, a platform for researchers in Transposable Elements

The TE Hub Consortium recently authored a commentary for移动DNAon theTE集线器, an open and collaborative platform, providing an entry point and reference site for researchers interested in Transposable Element (TE) diversity, identification, and annotation. While we eagerly await the publication in our journal, the authors participated in a sneak preview Q & A about the project.

Can you tell us a bit about the background and initiation of TE Hub?

哈迪·奎斯维尔(Hadi Quesneville):2019年5月,在FaseB移动DNA会议上,我们中的几个人会非正式地开会,并开始讨论我们面对的超负荷,并寻求我们在注释TES和存储TE注释及其参考序列方面的帮助。我们意识到我们已经到达了我们一个人都无法全面答复这一需求。我们需要为社区做些事情,以应对注释和生物信息学分析的瓶颈。我们建议让Te Bioinformic社区在协作平台上组织其专业知识,知识和工具,以帮助TE社区在不断扩展的工具,方法和资源的迷宫中找到自己的方式。在发送了一些电子邮件,松懈的消息和推文后,组织了第一次视频会议,以讨论我们如何构建它。

您何时以及为什么要编译重复数据库和重复工具的列表?

Tyler A. Elliott: I’ve had a long-standing interest in the existing resources for TEs, and like many others I’m sure, have had the thought that it would be useful to have a single point of reference for all of this information. The first step though was just understanding what databases and tools are available. Some of my team members at the CBG helped compile an initial list, which I then expanded greatly during my spare time. Most of this work happened during 2019, when I first shared the lists in a publicly-accessible document.

我还想编译有关用于对TES进行分类的各种系统以及这些系统的参考的信息,此外,除了各种命名元素的列表以及研究人员提出了较大的元素分组时。我希望人们更加意识到这些,希望当发现新元素可以将它们置于更大的背景下。

What have been key milestones and obstacles in setting up TE Hub?

Travis J. Wheeler: After kicking off bi-monthly meetings in June 2020, we quickly locked in a vision and laid out a concrete plan for developing and populating the website. This required setting up the technology stack (a heavily augmented version of the wiki.js package), followed by extensive content contributions to prepare the site for its initial release. We’ve finally reached the part that motivated the work: inviting others to get involved!

A central challenge has been establishing the scope of TE Hub – what role will it serve (and importantly, not serve) in the TE community. It’s really easy for the scope of a project to expand beyond supportable limits; we’ve worked hard to clearly define the purpose of TE Hub as supporting the access to TE resources, tools, and annotation methods.

我如何在TE Hub中了解新闻和公告?

Alexander Suh: Please follow us on Twitter@hub_tefor TE Hub announcements, join the #te-hub channel onTransposonsWorldwide Slack对于书面新闻,我们还进行了“枢纽更新”(通过上述频道宣布),这是一个每两个月的视频呼吁,要求新闻和公开讨论。

专家和新手如何参与为Te Hub做出贡献?

罗伯特·霍布利(Robert Hubley):实施TE Hub作为基于Wiki的网站实现了两个主要目标:它支持分散的社区指导的增长,并为具有广泛专业知识的贡献者提供机会。当前的主题领域只是该站点将随着​​个人贡献者的利益而发展的起点。此外,当前居住在该网站上的许多资源直接受益于新手和专家编辑的持续协助。如果某人不确定他们如何最好地帮助这项工作,请联系。

Where do you see TE Hub going in the short, medium, and long term?

Tony Heitkam: Currently, we are communicating TE Hub’s mission and are inviting researchers to join our effort. One of our communication efforts is the upcoming移动DNA评论;另一个是Faseb会议上的海报。

In the short to medium term, we aim to broadly expand the wiki. To ensure secure and dependable maintenance, we are planning secure baseline funding for the scaling of TE Hub. In the long term, we wish to put forward a framework for the translation and integration of tools and databases. Ideally, we hope to step past the listing of databases and tools, and to provide translations from one system/tool/classification scheme towards the other. We foresee that this will open the TE field further, making it easier for both novices and experts to procure TE annotations.

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